Positively charged lysozyme (LZ) and negatively charged pectin, were alternately deposited on the surface of the cellulose nanofibrous mats by layer-by-layer (LBL) self-assembly technique. Scanning electron microscopy images showed that the nanofibers were orderly and compactly arrayed after LBL. Besides, as the number of LZ/pectin bilayers increased, the average diameter of nanofibers increased. LZ has assembled on the cellulose mats successfully, which was confirmed by X-ray photoelectron spectroscopy analysis. Thermal gravimetric analysis results showed that the thermal properties of LZ/pectin films coated mats was better than that of the unmodified cellulose mats. Importantly, the results of the bacterial inhibition test for LBL structured mats and cellulose mats indicated that the nanofibrous mats coated by 10.5 LZ/pectin bilayers (with LZ on the outmost layer) possessed the strongest inhibitory effect against both Escherichia coli and Staphylococcus aureus.